scPDB - 3rfx entry

Protein Data Bank Entry:

PDB ID : 3rfx

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uronate dehydrogenase
ID:	URODH_AGRFC
AC:	Q7CRQ0
Organism:	Agrobacterium fabrum )
Reign:	Bacteria
TaxID:	176299
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	25.438
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.204	492.750

% Hydrophobic	% Polar
41.10	58.90
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	53.68 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
72.2229	39.3054	13.5769

Binding mode :

What is Poseview ?

2D View
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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O2A	N	GLN- 14	3.2	171.79	H-Bond (Protein Donor)	false
O1N	N	LEU- 15	2.97	167.47	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 34	2.68	172.17	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 34	3.4	120.47	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 34	2.73	166.34	H-Bond (Ligand Donor)	false
N3A	N	LEU- 35	3.33	137.43	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 51	2.88	145.15	H-Bond (Ligand Donor)	false
N1A	N	LEU- 52	2.81	174.46	H-Bond (Protein Donor)	false
O4B	N	GLY- 73	3.05	166.45	H-Bond (Protein Donor)	false
O1A	OG	SER- 75	2.86	122.21	H-Bond (Protein Donor)	false
O3	OG	SER- 75	3.12	162.35	H-Bond (Protein Donor)	false
O5B	O	HOH- 307	3.09	169.46	H-Bond (Protein Donor)	false